Earlier today, I was playing Ratchet and Clank 3 with hardware hacks enabled. I went to Planet Aquatos, and immediately upon arrival the game freaked the hell out and started flashing red and blue bars on the screen extremely rapidly. Pausing and unpausing the game then makes all the geometry invisible, and it still remains that way in software mode. Since it's hard to show off with a screenshot, I will provide a video link instead (Seizure warning!):

I was having the same exact issue at Aquatos (mine was even worse than this actually) but it seems that setting skidraw to 1 in hardware hacks and then loading the save (don't use savestates in this case) on Aquatos seems to have fixed it for now.